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Source code for galaxy.tool_shed.galaxy_install.update_repository_manager

"""
Determine if installed tool shed repositories have updates available in their respective tool sheds.
"""
import logging
import threading

from sqlalchemy import false

from galaxy import util
from galaxy.tool_shed.util.repository_util import get_tool_shed_status_for_installed_repository
from galaxy.tool_shed.util.shed_util_common import clean_dependency_relationships
from galaxy.util.tool_shed.common_util import get_tool_shed_url_from_tool_shed_registry
from galaxy.util.tool_shed.encoding_util import tool_shed_decode

log = logging.getLogger(__name__)


[docs]class UpdateRepositoryManager:
[docs] def __init__(self, app): self.app = app self.context = self.app.install_model.context # Ideally only one Galaxy server process should be able to check for repository updates. if self.app.config.enable_tool_shed_check: self.running = True self.sleeper = Sleeper() self.restarter = threading.Thread(target=self.__restarter) self.restarter.daemon = True self.app.application_stack.register_postfork_function(self.restarter.start) self.seconds_to_sleep = int(app.config.hours_between_check * 3600)
[docs] def get_update_to_changeset_revision_and_ctx_rev(self, repository): """Return the changeset revision hash to which the repository can be updated.""" changeset_revision_dict = {} tool_shed_url = get_tool_shed_url_from_tool_shed_registry(self.app, str(repository.tool_shed)) params = dict(name=str(repository.name), owner=str(repository.owner), changeset_revision=str(repository.installed_changeset_revision)) pathspec = ['repository', 'get_changeset_revision_and_ctx_rev'] try: encoded_update_dict = util.url_get(tool_shed_url, auth=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params) if encoded_update_dict: update_dict = tool_shed_decode(encoded_update_dict) includes_data_managers = update_dict.get('includes_data_managers', False) includes_datatypes = update_dict.get('includes_datatypes', False) includes_tools = update_dict.get('includes_tools', False) includes_tools_for_display_in_tool_panel = update_dict.get('includes_tools_for_display_in_tool_panel', False) includes_tool_dependencies = update_dict.get('includes_tool_dependencies', False) includes_workflows = update_dict.get('includes_workflows', False) has_repository_dependencies = update_dict.get('has_repository_dependencies', False) has_repository_dependencies_only_if_compiling_contained_td = update_dict.get('has_repository_dependencies_only_if_compiling_contained_td', False) changeset_revision = update_dict.get('changeset_revision', None) ctx_rev = update_dict.get('ctx_rev', None) changeset_revision_dict['includes_data_managers'] = includes_data_managers changeset_revision_dict['includes_datatypes'] = includes_datatypes changeset_revision_dict['includes_tools'] = includes_tools changeset_revision_dict['includes_tools_for_display_in_tool_panel'] = includes_tools_for_display_in_tool_panel changeset_revision_dict['includes_tool_dependencies'] = includes_tool_dependencies changeset_revision_dict['includes_workflows'] = includes_workflows changeset_revision_dict['has_repository_dependencies'] = has_repository_dependencies changeset_revision_dict['has_repository_dependencies_only_if_compiling_contained_td'] = has_repository_dependencies_only_if_compiling_contained_td changeset_revision_dict['changeset_revision'] = changeset_revision changeset_revision_dict['ctx_rev'] = ctx_rev except Exception as e: log.debug(f"Error getting change set revision for update from the tool shed for repository '{repository.name}': {str(e)}") changeset_revision_dict['includes_data_managers'] = False changeset_revision_dict['includes_datatypes'] = False changeset_revision_dict['includes_tools'] = False changeset_revision_dict['includes_tools_for_display_in_tool_panel'] = False changeset_revision_dict['includes_tool_dependencies'] = False changeset_revision_dict['includes_workflows'] = False changeset_revision_dict['has_repository_dependencies'] = False changeset_revision_dict['has_repository_dependencies_only_if_compiling_contained_td'] = False changeset_revision_dict['changeset_revision'] = None changeset_revision_dict['ctx_rev'] = None return changeset_revision_dict
def __restarter(self): log.info('Update repository manager restarter starting up...') while self.running: # Make a call to the Tool Shed for each installed repository to get the latest # status information in the Tool Shed for the repository. This information includes # items like newer installable repository revisions, current revision updates, whether # the repository revision is the latest installable revision, and whether the repository # has been deprecated in the Tool Shed. for repository in self.context.query(self.app.install_model.ToolShedRepository) \ .filter(self.app.install_model.ToolShedRepository.table.c.deleted == false()): tool_shed_status_dict = get_tool_shed_status_for_installed_repository(self.app, repository) if tool_shed_status_dict: if tool_shed_status_dict != repository.tool_shed_status: repository.tool_shed_status = tool_shed_status_dict self.context.flush() else: # The received tool_shed_status_dict is an empty dictionary, so coerce to None. tool_shed_status_dict = None if tool_shed_status_dict != repository.tool_shed_status: repository.tool_shed_status = tool_shed_status_dict self.context.flush() self.sleeper.sleep(self.seconds_to_sleep) log.info('Update repository manager restarter shutting down...')
[docs] def shutdown(self): if self.app.config.enable_tool_shed_check: self.running = False self.sleeper.wake()
[docs] def update_repository_record(self, repository, updated_metadata_dict, updated_changeset_revision, updated_ctx_rev): """ Update a tool_shed_repository database record with new information retrieved from the Tool Shed. This happens when updating an installed repository to a new changeset revision. """ repository.metadata = updated_metadata_dict tool_shed_url = get_tool_shed_url_from_tool_shed_registry(self.app, repository.tool_shed) clean_dependency_relationships(self.app, updated_metadata_dict, repository, tool_shed_url) # Update the repository.changeset_revision column in the database. repository.changeset_revision = updated_changeset_revision repository.ctx_rev = updated_ctx_rev # Update the repository.tool_shed_status column in the database. tool_shed_status_dict = get_tool_shed_status_for_installed_repository(self.app, repository) if tool_shed_status_dict: repository.tool_shed_status = tool_shed_status_dict else: repository.tool_shed_status = None self.app.install_model.context.add(repository) self.app.install_model.context.flush() self.app.install_model.context.refresh(repository) return repository
[docs]class Sleeper: """ Provides a 'sleep' method that sleeps for a number of seconds *unless* the notify method is called (from a different thread). """
[docs] def __init__(self): self.condition = threading.Condition()
[docs] def sleep(self, seconds): self.condition.acquire() self.condition.wait(seconds) self.condition.release()
[docs] def wake(self): self.condition.acquire() self.condition.notify() self.condition.release()